Integrative epigenetic and transcriptomic profiling of whole blood and fibroblasts in Hao-Fountain syndrome

Hao-Fountain syndrome (HAFOUS) is a rare autosomal dominant neurodevelopmental disorder caused by pathogenic USP7 variants. A diagnostic blood DNA methylation episignature has been established, yet the broader regulatory consequences of USP7 haploinsufficiency and their tissue specificity remain incompletely characterized.

We performed genome-wide DNA methylation profiling, RNA sequencing, and cis expression quantitative trait methylation (eQTM) analysis in whole blood (n = 9) and patient-derived skin fibroblasts (n = 4). Differential methylation was assessed and methylation-expression coupling within ±250 kb of each DMR. DMRs were further interpreted using BCOR, H2AK119ub1, and H3K27me3 ChIP-Rx datasets from neural models.

Blood reproduced the established USP7 hypermethylation episignature and yielded 17 significant DMRs, accompanied by modest numbers of differentially expressed genes and eQTMs. Fibroblasts displayed internally coherent regulatory patterns, including 2,143 nominal DMRs, 310 differentially expressed genes, and 559 significant eQTMs. Convergent methylation-expression changes prominently involved the HOXB cluster (HOXB3, HOXB5, HOXB6). Both blood- and fibroblast-derived DMRs showed significant enrichment for BCOR- and H2AK119ub1-marked regions, consistent with disruption of non-canonical PRC1.1-associated chromatin. Cross-tissue comparison revealed limited overlap, supporting marked tissue specificity in methylation-expression relationships.

USP7 haploinsufficiency is associated with a restricted set of regulatory loci enriched within PRC1-associated chromatin domains. Fibroblasts revealed coherent methylation and expression changes at developmental genes, whereas blood captured the diagnostic episignature and a smaller set of downstream regulatory alterations. Together, this dual-tissue integrative analysis refines the molecular consequences of reduced USP7 dosage and provides a framework for future mechanistic studies in disease-relevant cellular models.